Puzzle Pieces
by Maegfen
Summary: A series of missing scenes for Season 1 showing the progression of Tom and Rachel's relationship from strangers to reluctant allies and beyond. Canon compliant.
1. Episode 1 - Phase Six - Scene 1

**Author's note:** So, this was mainly started because webbieafan on tumblr prompted me to write some missing scenes and/ or back story for pretty much all of Season 1. The main point of it was to see the build-up in the relationship/tension between Tom and Rachel; little snippets of conversations and scenes that we didn't see on screen and the like :) So this will be a set of one-shots that will obviously link together, but will be completed with each one. So it's a WIP but not a WIP if that makes sense :D

I've got a few scenes already written out, so I'll try and update as often as possible for you guys!

If you have any ideas for missing scenes you want to see, feel free to send them my way. Please bear in mind that I'm going to keep this canon-compliant as much as I can, so there'll be no major romance between the two of them at this moment in time ;)

Let me know what you think, I hope you all enjoy!

* * *

**Chapter summary:** _"Rachel hates lying to the crew, to the Captain, sneaking around behind their backs, denying them the information that they would so desperately crave if they knew the truth."  
_**Chapter timeline: **Episode 1 - Phase Six (set between the departure from Norfolk and the attack by the Russians)

* * *

She doesn't really give a second thought to Captain Thomas Chandler and the crew of the Nathan James after they leave the harbor at Norfolk. Rachel's attention is focused solely on the cure, on finding a way to solve the puzzle of the virus and to hopefully saving humanity before it's completely eradicated.

She works every day with Quincy, desperately seeking the primordial strain, tracking the flight patterns of the Arctic Terns and constantly praying that luck will eventually turn in their favor. Rachel hates lying to the crew, to the Captain, sneaking around behind their backs, denying them the information that they would so desperately crave if they knew the truth. But she's knows she's right; what good will it do to tell these 217 men and women that the world is dying and there's probably very little that they can do about it…

The weather is bitterly cold, the freezing wind biting at her fingers as she works in the snow for hours on end but she tries not to notice it; the CDC had provided cold weather gear for her and Quincy as soon as word spread of their mission, so she takes solace in the fact that they were at least prepared to aid her in that respect, despite their continual protestations that they were both crazy. She can still hear the lingering laughter as she exited the final meeting with her boss all those weeks ago.

She briefly wonders how many of her colleagues remain alive and shoves the thought aside as quickly as it appears; there is no point in dwelling in the past, it will do her little good. She knows her mission; must focus purely on that or they are all doomed.

The fate of the world rests on her shoulders and it's a heavy burden, she knows and accepts this with a sorrowful heart. She tries talking to Quincy about it from time to time, but he has become standoffish in the last few weeks, almost withdrawn. He reveals no details of his troubles and she doesn't press him for information; she decides it is just his way of dealing with the immense pressure they are both under. Still, it would be nice to have _someone_ to talk to, but there is no one, not any more. They are alone, she and Quincy; two scientists against the world.

Rachel feels the burden increase with every day that passes. How may millions have died in the months they've been out here? She dreads to think, and she feels a horrible and traitorous sense of relief when she can't raise the CDC one freezing Monday morning three months into their trip. If she doesn't hear about the destruction and the chaos that is spreading across the globe, maybe she can just ignore it, even if just for a little while.

It doesn't stop the nightmares though.

A week later she walks carefully through the corridors of the ship going over the details of another unsuccessful day out on the ice. The lack of progress is frustrating, but Rachel knows change will come; it has to, _needs_ to.

She is still attempting to find her way around the large ship; there's so much grey and sameness that it's too easy to get turned around and disorientated. Rachel believes she's heading in the direction of the Mess Hall, but she isn't entirely sure. Still she carries on, sighing wearily and desperately craving a cup of tea. Nightmares have plagued her sleep again and it seems that the four hours she managed to get will have to suffice.

The corridors are eerily deserted as her footsteps echo around her, but then, it is late at night, and Rachel knows that crew numbers normally dwindle as the sun settles past the horizon. She finds a small amount of comfort in the quiet hum of the engine as she makes her way through yet another indiscriminate corridor.

Rachel rounds a corner and bumps into someone, and immediately steps back in order to apologize. She looks up, and meets the cool blue eyes of Captain Chandler himself.

"My apologies Captain," she says, glancing up at him and then averting her eyes, instead focusing her attention on a warning sign to her left. She's avoided the man for most of the last three months, feeling that if she got to know him, spend time with him, she'd feel obligated to reveal the truth about her mission and the fate of the outside world. She can't let that happen. She just can't - it's her burden to carry not his. She wonders, briefly, if he suffers from nightmares of his own.

"Doctor Scott," he replies simply, and he stares at her then, a determined look on his face and his arms folding across his chest. Rachel panics, wondering if he wants to strike up a conversation with her in the middle of the night in a deserted corridor.

Thankfully, he doesn't, and she breathes out a small sigh of relief when he just shakes his head and gestures for her to pass by him in the thin corridor. She offers the man a small and sincere smile, and receives one in return as she goes on her way. Rachel doesn't look back, afraid that she'll be overwhelmed again and spill her secrets to the quiet leader of the Nathan James.

Rachel stands resolutely by her decision to not give him another thought - the Nathan James is merely a convenient vessel for her task, it's Captain not the person who needs to deal with her issues, no matter how overwhelming and horrific they may be. Her mission is paramount, she tells herself; there is no point in getting attached to Captain Thomas Chandler.


	2. Episode 1 - Phase Six - Scene 2

**Author's note:** While this fic will definitely look at the growing relationship between Tom and Rachel, there may be a couple of missing scenes that don't feature either of them. I figured, if I'm going to write a missing scene fic, I may as well go all out and fill in some of the other gaps. I hope people don't find that too annoying; trust me, the Tom/Rachel aspect will be a prominent part of this :)

I'm up to 15 prospective scenes/chapters at the moment, with new ideas appearing all the time; so this could end up being a monster...

* * *

**Chapter summary:** "Rachel sighs, feeling a new set of troubles weigh down on her already heavy shoulders. She'd chosen to bear this burden, had done so willingly, but now it feels like it's too much."  
**Chapter timeline:** Episode 1 - Phase Six (after Rachel reveals the truth to Tom following the Russian attack)

* * *

She watches as Captain Chandler follows his XO out of the hanger deck to talk to the President. Rachel knows that Geller died a couple of months ago and that Chambers was running the country following the Vice President's death a few short days later; she wonders how much information the former Speaker of the House will reveal about exactly _why_ the Nathan James has been stationed in the Arctic for the last 4 months. A shudder passes through her as she remembers the look of anger, of disgust, that had crossed the Captain's faced when she'd initially revealed the truth. She doesn't blame him. She'd had over 6 months to get used to the idea of a global pandemic; Chandler had barely had four minutes before he'd been called away to talk to the President.

Her return to the lab is a slow process. Members of the crew eye her suspiciously as she passes through the maze of corridors. Word of the nature of the Russian attack is obviously spreading throughout the vessel and details of her involvement seem be interwoven with each new telling of the story. Rachel sighs, feeling a new set of troubles weigh down on her already heavy shoulders. She'd chosen to bear this burden, had done so willingly, but now it feels like it's too much. She craves tea and peace and an escape; none of which are possible right now. She longs for the moment when she can rest.

She continues to analyse her conversation with the Captain, trying to decipher every nuance and detail of their words and glances as a way to distract herself from the accusing eyes that glare at her on her journey.

She feels a rush of disappointment flow through her as she recalls the moment that he got it, that he finally _understood_ just what what happening in the world outside, when he replaced his anger with something resembling fear and confusion. Rachel feels like she's let him down, despite the fact that she's barely spoken to him since they left Norfolk. A couple of awkward, stilted conversations in corridors late at night do_not_ count.

The look on Chandler's face as he'd come to terms with the implications of her words flash across her mind again; it was the expression of a man whose whole world had fallen from beneath him. Rachel feels a momentary rush of sadness that she caused that expression to grace his face. She'd been honest when she'd said she wished he could have found out another way...

Her side suddenly burns from the bullet wound, the graze aching and pulling as she makes her way through the narrow corridors. She reminds herself that she'll need to revisit the ship's doctor in order to have the bandage changed at some point. Still, it can wait; she has her samples and they need analyzing. Rachel crosses her fingers, a childish gesture she knows, but she hopes that their troubles have all been worth it, that Quincy and herself had finally located the primordial strain. Judging by Captain Chandler's expression when he left, the odds weren't looking good that they'd be granted another day on the ice; even _without_ the now inevitable threat of Russian attack.

Quincy is sitting at the desk as she re-enters the lab, his eyes focused on the computer screen in front of him. Rachel notes that he still seems oddly quiet, pen tapping idly away on the table as he re-reads the previous day's analysis. He turns slowly as soon as he hears the metal door scrape open and he faces her, concern etched across his face.

"Are you ok?" he asks, standing and moving towards her. Rachel feels his hand touch her shoulder and she struggles to hold back a wave of tears._ It's too much_, she thinks,_ it's all too much. I can't do this..._

"He know," she utters bluntly, straightening up and putting on the appearance of someone who is strong, who can handle this immense pressure. She looks up at her partner, hoping to draw the same strength that she has from him over the last 10 years. They've never been in a situation _this_ bad before, but Quincy's presence has always anchored her somehow; she wouldn't know what to do with herself if he wasn't here to help her.

"Who knows? Knows what?" Quincy is confused, and he turns his attention to the door, as if the opening to the rest of the ship holds all the answers.

"The Captain," Rachel clarifies, sighing as relief starts to flow through her. She's not sure why, but just telling Quincy this is enough to lift some of the weight off her weary shoulders. "Captain Chandler knows about the virus, about the world outside, everything..."

She expects Quincy to rage, to be angry at the fact that their mission is blown. But instead, all he does is nod once and Rachel hears him mutter "good" quietly under his breath.

He's silent for a minute, eyes shifting between her, the samples and the eerily quiet lab. Rachel closes her eyes briefly and listens for the now familiar hum of the engines.

Eventually, Quincy speaks again, his voice quiet but demanding. "What do we do now?"

She shrugs half-heartedly as she moves to open the sample case. Her thumbs fiddle idly with the locks, fingers gliding over the cool metal; anything will serve as a welcome distraction for her at the moment...

"Rachel?" he asks, hand reaching out for her shoulder again, the touch enough to get her full attention. "What do we do?"

She shakes her head, coming out of her thoughts and looks up at him.

"We find the cure." She states simply, gesturing towards the case she still clutches in her hand. The metal of the handle is cool against her palm, but she ignores it. They finally have a breakthrough and now she and Quincy can get started on saving the world.

She puts Captain Chandler out of her mind for the moment and focuses on setting up the next level of analysis. The answers to the world's problems could be inside these samples and nothing; not the freezing temperatures, not the pain in her side, not the disappointment of a man she barely knows, should dissuade her from completing her mission.


	3. Episode 1 - Phase Six - Scene 3

**Author's note: **Here's the next chapter for you all; I hope you enjoy :) Apologies for the slightly awkward pov change in this chapter; Tom and Rachel both wanted to contribute to the conversation!

* * *

**Chapter summary: **"He feels like he's running on empty, like he's relying on the same depleted fuel reserves that the ship is."  
**Chapter timeline:** Episode 1 - Phase Six (after they discover the Italian cruise ship floating adrift in the ocean)

* * *

She doesn't initially notice his arrival in the warm hanger bay. She's so focused on gathering the latest set of results that it isn't until Captain Chandler coughs slightly that she realizes that anyone else is in the room at all. Quincy had disappeared an hour ago to get some well-earned rest, leaving her with nothing but a warning to "not stay up too late."

Quincy knows what she's like, and will inevitably reappear in another couple of hours to shepherd her off to her own uncomfortable bunk; he's had to complete the same routine in every isolated camp and hospital they've ever worked in.

She places the pipette and test tube carefully back in the rack, the primordial strain sitting in the plastic, completely unaware of its importance in the potential salvation of all mankind.

Captain Chandler is waiting patiently for her to finish, although Rachel is still concerned by the look that crosses his face. Since the nuclear attack by the Russian's she's barely seen him, but he looks harried now, focused but concerned. She wonders briefly if his shoulders feel as heavy as her own.

Rachel moves to stand by the wall of her plastic tomb, leaning almost casually against the desk that rests near the back wall.

The Captain sighs, and glances around at the lab behind her. He's rarely been down here, and Rachel considers whether she should offer him a guided tour by way of an olive branch. She dismisses the thought almost immediately; Captain Chandler has better things to do than pander to her crude attempts at an apology.

"There's a ship," he starts eventually, folding his arms across his chest and eyeing her warily. "We need to go across and get fuel and supplies."

"Okay..." Rachel replies slowly, unsure of why he's come to see her at all. She's still encased in the lab, the plastic bubble making her feel like she's in a zoo - constantly under scrutiny from the visitors that enter the hanger bay. "I fail how to see how I can be of assistance with that. I'm sure it hasn't slipped your notice that I'm a doctor not a soldier."

She doesn't intend to be short with him, but her tone comes out harsher than she expected. It doesn't seem to phase the man in front of her though, who merely glances at her and nods it what seems to be understanding.

There's an awkward silence hanging between them now. Rachel has an inkling that the Captain requires her thoughts on the virus, but he seems unable, or even unwilling, to completely broach the subject with her.

* * *

Tom sighs and sweeps a hand through his hair, the action purely a means to break the awkwardness that's suddenly appeared in the hanger bay. There's been a tension between them since their confrontation over the virus, but he senses that her slightly irritable tone isn't a result of their unease with each other. Instead, he notes that Doctor Scott looks weary, tired, as if she has the world on her shoulders. He shares her sentiments. He feels like he's running on empty, like he's relying on the same depleted fuel reserves that the ship is. He longs for a cup of coffee and his bunk, but he's been in the Navy long enough to know when a long night is ahead. The exhaustion and prospect of no sleep that night was inevitable from the moment the Russian's sent a nuclear missile over their heads.

He glances at the doctor once more, noting her confusion. Clearly she's wondering why he's made the effort to come here; she isn't a soldier, but what she _can_ offer will hopefully save the lives of everyone aboard the Nathan James and the remaining human population.

He considers his words carefully, knowing that he has no jurisdiction over her, is unable to issue her an order. But he _needs_ her, requires her expertise to ensure the safety of his crew on their mission.

"We have reason to believe that the ship has been hit by the virus. I need you to brief the crew on what to expect. In fact," he says, pausing to glance at her more intently, "I'd like you to join us on the mission."

He's taking a huge risk, he knows this. From what she's told him, she and Doctor Tophet may be the only ones who could hope to find a cure for the virus, and by taking her along he's risking the loss of one of those people. Still, Tom knows that he and his men will have _no_ idea of what to expect if they get across to the abandoned cruise ship - any help with preparation would be extremely beneficial.

"I'm not trained..."

"I know," he says reassuringly. He understands her hesitation; she's already had more guns fired at her in the last 24 hours than she probably ever has in her life. "We'll keep eyes out for you. The first sign of danger and we'll pull you out. But I need your expertise out there; I've got no idea what my men could be walking into. You said yourself you've been aware of the dangers of the virus for months; you're the foremost expert on it."

Doctor Scott sighs resignedly, as if knowing that really, she has no choice in the matter.

"I understand," she mumbles eventually, turning to look at him from inside her plastic cage. "I'm just finishing a round of analysis on the primordial strain I collected yesterday; I need half an hour to complete them and prepare what I need to brief your crew."

Tom nods, knowing that this first step, this first sign of trust in her, will go a long way. He may not see eye-to-eye with Doctor Scott, especially after her decisions in the Arctic, but being able to work alongside her is essential.

"That's fine," he replies softly, sparing another glance at the equipment behind her. He knows that this lab could potentially house the solution to saving the world; it's a heady thought. "I'll send someone down shortly; they'll escort you to the wardroom where you can brief the officers when you're ready."

Doctor Scott doesn't reply, just nods and gives him a small smile. It's a simple gesture, but it's a start.

The anger and frustration that he feels towards her starts to ebb away just a little and his last sight of her before he disappears to find Mike is her leaning over a microscope, deep in thought, concentration evident on her face under the cold plastic visor of her mask.

Maybe, just _maybe_, he thinks, they might be able to save the world after all.


End file.
